In [2]:
source('/home/meisl/bin/bin/bin/source.R')
In [3]:
load('slide-seq.RData')
In [ ]:
In [5]:
sam =c('HP1','HP2','HP3','HP4','Benign01','Benign02','Benign03','Benign04','Tumor01','Tumor02','Tumor08','Tumor07')

for (i in sam){
femb = alle[[i]]

gg1 = embeddingPlot(femb,,groups = ano_l1f ,palette = anoM.palf,plot.na=F,size=0.1,alpha=0.5,show.legend = FALSE,mark.groups = F,title=i)
gg1 = embForMat(gg1)+theme(legend.position = 'none')

#ggsave(paste(i,'.all.pdf'),gg1,width = 3,height=3.1)

print(gg1)


}
In [6]:
ano.se2 = ano_l1f
lev = unique(ano.se2)
#ano.se2= ano.se[!grepl('Benign03|Benign04',names(ano.se))]
ano.se2 = as.factor(ano.se2)
lev =c("Epithelial" ,"Endothelial", "Fibroblasts" ,"Pericytes"  , "Mast cells"  ,  "myeloid cells" ,"PDC" ,"B cells","Tcell"    )

ano.se2 = ordered(ano.se2,levels =lev)

source('/d0-mendel/home/meisl/bin/FunctionLib/Lib/ploty.Dotplot.r')

gs=c("KLK4" ,"KLK3"  ,  "KLK2" , "ACPP"  , "RAMP3","VWF","PLVAP",'IGFBP3','FN1','LUM','MMP2','MTIM','ACTA2',"CPA3","TPSAB1","C1QA","C1QB","S100A8","S100A9","IRF4",'IRF7','CD79B','','MS4A1','CD3D')#

gs =intersect(gs,rownames(expa))
library(cowplot)
source('/d0-mendel/home/meisl/bin/FunctionLib/Lib/ploty.Dotplot2.r')
cname=names(ano.se2)
cname = intersect(cname,colnames(expa))
p=Dotfig(gs,expa[,cname],ano.se2[cname],cols = c("blue","white", "red"))
p1=p+xlab('')+ylab('')#+theme(legend.position = 'top')
p1

Attaching package: ‘cowplot’


The following object is masked from ‘package:ggpubr’:

    get_legend



[1] "blue"
[1] "white"
[1] "red"
In [13]:
epi
  1. 'Epithelial_Basal'
  2. 'Epithelial_Club'
  3. 'Epithelial_Hillock'
  4. 'Epithelial_Luminal'
  5. 'Tumor'
In [7]:
# Epithelial cells
sam =c('HP1','Benign04','Tumor08','Tumor02')

fl = lapply(sn(sam), function(i) {
  gg1 = embeddingPlot(alle[[i]],groups = ano_l2[ano_l2 %in% epi] ,palette = function(n) return(cols_l1[epi][1:n]),plot.na = F,size = 0.3,alpha = 0.8,show.legend = FALSE,mark.groups = F,title = i)
  embForMat2(gg1)
})


b = cowplot::plot_grid(plotlist=fl,ncol=2)
b
In [14]:
# stromal cells
stromal
  1. 'Endothelial cells-1'
  2. 'Endothelial cells-2'
  3. 'Pericytes-1'
  4. 'Pericytes-2'
  5. 'Fibroblasts'
In [11]:
sam =c('HP1','Benign04','Tumor08','Tumor02')

fl = lapply(sn(sam), function(i) {
  gg1 = embeddingPlot(alle[[i]],groups = ano_l2[ano_l2 %in% stromal] ,palette = function(n) return(cols_l1[stromal][1:n]),plot.na = F,size = 0.3,alpha = 0.8,show.legend = FALSE,mark.groups = F,title = i)
  embForMat2(gg1)
})


b = cowplot::plot_grid(plotlist=fl,ncol=2)
b
In [15]:
immune
  1. 'B cells'
  2. 'Macrophage'
  3. 'Tcell'
  4. 'Monocytes'
  5. 'plasma cells'
In [12]:
sam =c('HP1','Benign04','Tumor08','Tumor02')

fl = lapply(sn(sam), function(i) {
  gg1 = embeddingPlot(alle[[i]],groups = ano_l2[ano_l2 %in% immune] ,palette = function(n) return(cols_l1[immune][1:n]),plot.na = F,size = 0.8,alpha = 0.8,show.legend = FALSE,mark.groups = F,title = i)
  embForMat2(gg1)
})


b = cowplot::plot_grid(plotlist=fl,ncol=2)
b
In [ ]:
In [16]:
ano.se2 = ano_l2[ano_l2 %in% epi]
lev = unique(ano.se2)
#ano.se2= ano.se[!grepl('Benign03|Benign04',names(ano.se))]
ano.se2 = as.factor(ano.se2)
lev = c("Tumor"     ,          "Epithelial_Luminal"  , "Epithelial_Basal"  ,"Epithelial_Club"  ,  "Epithelial_Hillock")
ano.se2 = ordered(ano.se2,levels =lev)

source('/d0-mendel/home/meisl/bin/FunctionLib/Lib/ploty.Dotplot.r')

gs=c("PCA3","AMACR","ERG",'CACNA1D','COL9A2','PHGR1','GCNT1','FABP5','PHGR1'  ,'AR',"KLK4" ,"KLK3"  ,  "KLK2" , "ACPP","TP63"  ,  "KRT14" ,  "KRT5"  ,"SCGB1A3" ,'WFDC2','LCN2' ,'MMP7','KRT4','TACSTD2',"KRT13",'S100A16')

gs =intersect(gs,rownames(expa))
library(cowplot)
source('/d0-mendel/home/meisl/bin/FunctionLib/Lib/ploty.Dotplot.r')
cname=names(ano.se2)
cname = intersect(cname,colnames(expa))
p=Dotfig(gs,expa[,cname],ano.se2[cname],cols = c("blue","white", "red"))
p1=p+xlab('')+ylab('')#+theme(legend.position = 'top')
p1

[1] "blue"
[1] "white"
[1] "red"
In [19]:
# plot tumor signatures
In [21]:
i = 'Tumor02'

tmp1 =alle[[i]]

tmp = ano_l2

epi = tmp[grepl(i,names(tmp))]

cname = names(epi[epi =='Tumor'])
linetype <- 1; color='red';

tmp = tmp1[rownames(tmp1) %in% cname,]
kd <- ks::kde(tmp, compute.cont=TRUE)
lcn3 <- with(kd, contourLines(x=eval.points[[1]], y=eval.points[[2]],z=estimate, levels=cont["20%"])[[1]])
cn3 <- geom_path(aes(x, y), data=data.frame(lcn3),linetype = linetype , color=color);
gg2=slide.exps(alle,sami='Tumor02',cell=epi,gene=c('PCA3','AMACR','ERG','GCNT1','CACNA1D','FABP5','COL9A2'),title='Tumor signature')

gg2 = gg2+cn3+theme(legend.position = 'right')

gg2
In [ ]:
In [22]:
i = 'Tumor01'

tmp1 =alle[[i]]

tmp = ano_l2

epi = tmp[grepl(i,names(tmp))]

cname = names(epi[epi =='Tumor'])
linetype <- 1; color='red';

tmp = tmp1[rownames(tmp1) %in% cname,]
kd <- ks::kde(tmp, compute.cont=TRUE)
lcn3 <- with(kd, contourLines(x=eval.points[[1]], y=eval.points[[2]],z=estimate, levels=cont["20%"])[[1]])
cn3 <- geom_path(aes(x, y), data=data.frame(lcn3),linetype = linetype , color=color);
gg2=slide.exps(alle,sami='Tumor01',cell=epi,gene=c('PCA3','AMACR','ERG','GCNT1','CACNA1D','FABP5','COL9A2'),title='Tumor signature')

gg2 = gg2+cn3+theme(legend.position = 'right')

gg2
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